feat: job arrays

snakemake_executor_plugin_slurm/__init__.py

@@ -6,6 +6,7 @@
 import atexit
 import csv
 from io import StringIO
+from itertools import groupby
 import os
 from pathlib import Path
 import re
@@ -168,6 +169,20 @@ def warn_on_jobcontext(self, done=None):
     def additional_general_args(self):
         return "--executor slurm-jobstep --jobs 1"
 
+    def run_jobs(self, jobs: List[JobExecutorInterface]):
+        for rule_name, group in groupby(jobs, key=lambda job: job.rule.name):
+            same_rule_jobs = list(group)  # Materialize the generator
+            if len(same_rule_jobs) == 1:
+                self.run_job(same_rule_jobs[0])
+            else:
+                # TODO submit as array
+                # share code with run_job
+
+                # TODO in the future: give a hint to the scheduler to select preferably
+                # many jobs from the same rule if possible, in order to have
+                # more efficient array jobs. This should be somehow tunable, because
+                # it might contradict other efficiency goals.
+                ...
     def run_job(self, job: JobExecutorInterface):
         # Implement here how to run a job.
         # You can access the job's resources, etc.